search

pnnl / leapR

BSD 3-Clause "New" or "Revised" License
17 stars 5 forks source link

Fix implementation of 'minsize' restriction for enrichment_in_sets (Script: enrichment_in_groups.R) #43

Open HarkiratSohi opened 1 year ago

HarkiratSohi commented 1 year ago

I noticed the output for enrichment_in_sets doesn't restrict the analysis to the default "minsize = 5" (# of members in the overlap of interest?) or any other specified value of minsize. Currently, there is no check for minsize for the code corresponding to the Fisher's test in enrchiment_in_groups.R.

Need to add checking of minsize (input parameter specified in the enrichment_in_sets method in leapR) in enrichment_in_groups.R for the block of code under " if (method == "fishers"){ "

HarkiratSohi commented 1 year ago

Also add clear documentation for what minsize represents.